Harmful algal blooms (HABs) exert strongly negative impacts on coastal oceans, lakes, rivers, and municipal drinking supplies world-wide. These can be seen, for example, either directly though production and release of potent neurotoxins and/or through massive die-offs that induce anoxic conditions and extensive fish-kills. Contamination of shellfish with toxins produced by HABs continues to be an ongoing concern for the fisheries, aquaculture industry, and research fields as the HABs cause ocean closures, sale bans, and consumption restrictions. Not only are HABs harmful for human consumers, but the toxic blooms are often devastating to the ecosystem and to a large variety of marine organisms. HABs can have a direct, potentially fatal, effect on humans.
Consumption of shellfish contaminated with algal toxins can cause paralytic shellfish poisoning (PSP) which can be potentially fatal. Several types of toxins associated with HABs have been characterized including saxitoxin, neosaxitoxin, gonyautoxin, decarbamoyl saxitoxin, among others, particularly produced by plankton belonging to the genera Alexandrium, Gymnodinium, Pyrodinium, and Pseudo-nitzschia. 
Remarkably, there remains no simple, straightforward, precise, rapid, and low-cost technique to identify the diverse array of HAB cells and their toxins from water samples. As such, the ability to characterize the plankton community at the species level provides an immensely valuable index of ecosystem condition and how it may be changing relative to climate change and ocean acidification. Identification of plankton on the spatial and temporal scales necessary to use diversity and abundance as an environmental index is a very difficult problem and goes well beyond technicians with plankton nets or filtering devices and laboratory microscopes and high-performance liquid chromatography (HPLC) and liquid chromatography-mass spectrometry (LC-MS) analytical instrumentation. A truly useful plankton index of environmental health and water quality requires real-time, automated approaches to species identification and quantification of potential toxins on temporal/spatial scales of seconds and meters. Such instruments must provide precise and accurate answers quickly and be sufficiently inexpensive to be available on every swimming beaches and in every municipal reservoir in the country. Instruments need to be in the water, sampling continuously, and sending their processed data products to managers and scientists worldwide without delay. Additionally, they must be robust to corrosion, biofouling, and mechanical damage. Such systems need be sufficiently intelligent to understand and separate background noise from a true signal, and capable to parse and integrate a variety of information from a variety of sources.
Therefore, there exists a need for new systems and methods for accurately identifying species and strains of algae pertaining to HABs on a real-time and accurate basis.